On the computational complexity of sequence design problems

Inverse protein folding concerns the identification of an amino acid sequence that folds to a given structure. Sequence design problems attempt to avoid the apparent difficulty of inverse protein folding by defining an energy that can be minimized to find protein-like sequences. The authors evaluate the practical relevance of two sequence design problems by analyzing their computation complexity. They show that the canonical method of sequence design is intractable, and describe approximation algorithms for this problem. The authors also describe an efficient algorithm that exactly solves the grand canonical method. The analysis shows how sequence design problems can fail to reduce the difficulty of the inverse protein folding problem, and highlights the need to analyze these problems to evaluate their practical relevance

Lattice and off-lattice side chain models of protein folding: Linear time structure prediction better than 86% of optimal

This paper considers the protein structure prediction problem for lattice and off-lattice protein folding models that explicitly represent side chains. Lattice models of proteins have proven extremely useful tools for reasoning about protein folding in unrestricted continuous space through analogy. This paper provides the first illustration of how rigorous algorithmic analyses of lattice models can lead to rigorous algorithmic analyses of off-lattice models. The authors consider two side chain models: a lattice model that generalizes the HP model (Dill 85) to explicitly represent side chains on the cubic lattice, and a new off-lattice model, the HP Tangent Spheres Side Chain model (HP-TSSC), that generalizes this model further by representing the backbone and side chains of proteins with tangent spheres. They describe algorithms for both of these models with mathematically guaranteed error bounds. In particular, the authors describe a linear time performance guaranteed approximation algorithm for the HP side chain model that constructs conformations whose energy is better than 865 of optimal in a face centered cubic lattice, and they demonstrate how this provides a 70% performance guarantee for the HP-TSSC model. This is the first algorithm in the literature for off-lattice protein structure prediction that has a rigorous performance guarantee. The analysis of the HP-TSSC model builds off of the work of Dancik and Hannenhalli who have developed a 16/30 approximation algorithm for the HP model on the hexagonal close packed lattice. Further, the analysis provides a mathematical methodology for transferring performance guarantees on lattices to off-lattice models. These results partially answer the open question of Karplus et al. concerning the complexity of protein folding models that include side chains

FILM GROWTH ON ALUMINUM IN HIGH-TEMPERATURE WATER

Film growths on aluminum and two aluminum-1 wt.% nickel alloys in water at 250 and 350 deg C were studied. It was found that oxide growth does not advance on a uniform front but, to the contrary, the advancing surface contains many outcrops in the form of thin platelets, chunky outcrops, and whiskers. With both the pure metal and the alloys considerable intergranular attack was observed. The general corrosion product was usually more uniform in crystal size when formed on the pure metal, but variations in crystal size were observed on both aluminum and alloys with varying features of the metal surface. The roughness of the general oxide surface (includlng outcrops) was found to increase rapidly to about 0.2 micron and then remain relatively constant with increasing film thickness. The composition of films formed under all investigated conditions, except one, was found to be boehmite ( alpha -Al/sub 2/O/sub 3/- H/sub 2/O). This exception was films carried by the alloy specimens after testing for 32 days at 350 deg C. In this case the main corrosion film was still boehmite, but in addition the outer surface supported long needles of diaspore ( beta -Al/sub 2/ O/sub 3/- H/sub 2/O). (auth

Design and Operation of Gravity or Surface Systems (Chapter 13)

Surface irrigation uses open channel flow to spread water over a field. The driving force in such systems is gravity and hence the alternate term, gravity flooding. Once distributed over the surface of the field and after it has entered the soil, water is often redistributed by forces other than gravity. Surface irrigation systems generally require a smaller initial investment than do other types of irrigation systems. However, this is not always the case, especially if extensive land forming is needed for an efficient system. In fact, the need for extensive land forming is one of the main reasons why other types of irrigation systems have been developed

Thermodynamics of Large-N_f QCD at Finite Chemical Potential

We extend the previously obtained results for the thermodynamic potential of hot QCD in the limit of large number of fermions to non-vanishing chemical potential. We give exact results for the thermal pressure in the entire range of temperature and chemical potential for which the presence of a Landau pole is negligible numerically. In addition we compute linear and non-linear quark susceptibilities at zero chemical potential, and the entropy at small temperatures. We compare with the available perturbative results and determine their range of applicability. Our numerical accuracy is sufficiently high to check and verify existing results, including the recent perturbative results by Vuorinen on quark number susceptibilities and the older results by Freedman and McLerran on the pressure at zero temperature and high chemical potential. We also obtain a number of perturbative coefficients at sixth order in the coupling that have not yet been calculated analytically. In the case of both non-zero temperature and non-zero chemical potential, we investigate the range of validity of a scaling behaviour noticed recently in lattice calculations by Fodor, Katz, and Szabo at moderately large chemical potential and find that it breaks down rather abruptly at $\mu_q \gtrsim \pi T$, which points to a presumably generic obstruction for extrapolating data from small to large chemical potential. At sufficiently small temperatures $T \ll \mu_q$, we find dominating non-Fermi-liquid contributions to the interaction part of the entropy, which exhibits strong nonlinearity in the temperature and an excess over the free-theory value.Comment: 18 pages, 7 figures, JHEP style; v2: several updates, rewritten and extended sect. 3.4 covering now "Entropy at small temperatures and non-Fermi-liquid behaviour"; v3: additional remarks at the end of sect. 3.4; v4: minor corrections and additions (version to appear in JHEP

BAs and boride III-V alloys

Boron arsenide, the typically-ignored member of the III-V arsenide series BAs-AlAs-GaAs-InAs is found to resemble silicon electronically: its Gamma conduction band minimum is p-like (Gamma_15), not s-like (Gamma_1c), it has an X_1c-like indirect band gap, and its bond charge is distributed almost equally on the two atoms in the unit cell, exhibiting nearly perfect covalency. The reasons for these are tracked down to the anomalously low atomic p orbital energy in the boron and to the unusually strong s-s repulsion in BAs relative to most other III-V compounds. We find unexpected valence band offsets of BAs with respect to GaAs and AlAs. The valence band maximum (VBM) of BAs is significantly higher than that of AlAs, despite the much smaller bond length of BAs, and the VBM of GaAs is only slightly higher than in BAs. These effects result from the unusually strong mixing of the cation and anion states at the VBM. For the BAs-GaAs alloys, we find (i) a relatively small (~3.5 eV) and composition-independent band gap bowing. This means that while addition of small amounts of nitrogen to GaAs lowers the gap, addition of small amounts of boron to GaAs raises the gap (ii) boron ``semi-localized'' states in the conduction band (similar to those in GaN-GaAs alloys), and (iii) bulk mixing enthalpies which are smaller than in GaN-GaAs alloys. The unique features of boride III-V alloys offer new opportunities in band gap engineering.Comment: 18 pages, 14 figures, 6 tables, 61 references. Accepted for publication in Phys. Rev. B. Scheduled to appear Oct. 15 200